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Yorodumi- PDB-3we5: Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3we5 | ||||||
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Title | Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita | ||||||
Components | Ubiquitin conjugating enzyme | ||||||
Keywords | LIGASE / alpha / beta / ubiquitin conjugating enzyme E2 / ubiquitin binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrocybe aegerita (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Li, D.F. / Feng, L. / Wang, D.C. / Liu, W. | ||||||
Citation | Journal: To be Published Title: Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita Authors: Li, D.F. / Feng, L. / Wang, D.C. / Liu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3we5.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3we5.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 3we5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3we5_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 3we5_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 3we5_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 3we5_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/3we5 ftp://data.pdbj.org/pub/pdb/validation_reports/we/3we5 | HTTPS FTP |
-Related structure data
Related structure data | 2fo3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19162.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrocybe aegerita (fungus) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: H9CTH3, ubiquitin-protein ligase #2: Chemical | ChemComp-ACY / | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.2M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.45 Å / Num. all: 37328 / Num. obs: 37008 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3958 / Rsym value: 0.204 / % possible all: 72.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FO3 Resolution: 1.7→34.641 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.318 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→34.641 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26
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